10-44934719-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001123376.3(TMEM72):​c.413C>A​(p.Ala138Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

TMEM72
NM_001123376.3 missense

Scores

2
17

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 1.06
Variant links:
Genes affected
TMEM72 (HGNC:31658): (transmembrane protein 72) This gene encodes a transmembrane protein which may be expressed specifically in the kidney. [provided by RefSeq, Sep 2016]
TMEM72-AS1 (HGNC:27349): (TMEM72 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07229194).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM72NM_001123376.3 linkc.413C>A p.Ala138Asp missense_variant Exon 5 of 5 ENST00000389583.5 NP_001116848.1 A0PK05-1
TMEM72NM_001345926.2 linkc.59C>A p.Ala20Asp missense_variant Exon 4 of 4 NP_001332855.1 A0PK05-2
TMEM72-AS1NR_033842.1 linkn.99-11493G>T intron_variant Intron 1 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM72ENST00000389583.5 linkc.413C>A p.Ala138Asp missense_variant Exon 5 of 5 1 NM_001123376.3 ENSP00000374234.4 A0PK05-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
-
James Howe Lab, University of Iowa Hospital and Clinics
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.070
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
15
DANN
Uncertain
0.97
DEOGEN2
Benign
0.043
T;.
Eigen
Benign
-0.36
Eigen_PC
Benign
-0.40
FATHMM_MKL
Benign
0.070
N
LIST_S2
Benign
0.47
T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.072
T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Uncertain
2.4
M;.
PrimateAI
Benign
0.34
T
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.063
Sift
Benign
0.22
T;D
Sift4G
Benign
0.15
T;T
Polyphen
0.28
B;.
Vest4
0.20
MutPred
0.19
Loss of MoRF binding (P = 0.0391);.;
MVP
0.081
MPC
0.25
ClinPred
0.68
D
GERP RS
4.3
Varity_R
0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587777896; hg19: chr10-45430167; API